Hunner‐type interstitial cystitis (HIC) is a chronic inflammatory disease of the urinary bladder with an unknown etiology. We conducted comprehensive immunogenomic profiling of bladder specimens obtained by biopsy and cystectomy from 37 patients with HIC. Next‐generation RNA sequencing demonstrated abundant plasma cell infiltration with frequent light chain restriction in HIC‐affected bladder tissue. Subsequent analysis of the B‐cell receptor repertoire revealed spatial and temporal expansion of B‐cell clones. The extent of B‐cell clonal expansion was significantly correlated with the gene expression levels of TNFSF13 and TNFSF13B , which encode APRIL and BAFF, respectively. These findings indicate that APRIL and BAFF are the key regulators of clonal B‐cell expansion in HIC and might serve as therapeutic targets in this debilitating disease. © 2024 The Author(s). The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.

Neuroendocrine carcinoma (NEC) is a highly aggressive subtype of the neuroendocrine tumor with an extremely poor prognosis. We have previously conducted a comprehensive genomic analysis of over 100 cases of NEC of the gastrointestinal system (GIS‐NEC) and unraveled its unique and organ‐specific genomic drivers. However, the epigenomic features of GIS‐NEC remain unexplored. In this study, we have described the epigenomic landscape of GIS‐NEC and small cell lung carcinoma (SCLC) by integrating motif enrichment analysis from the assay of transposase‐accessible chromatin sequencing (ATAC‐seq) and enhancer profiling from a novel cleavage under targets and tagmentation (CUT&Tag) assay for H3K27ac and identified ELF3 as one of the super‐enhancer–related transcriptional factors in NEC. By combining CUT&Tag and knockdown RNA sequencing for ELF3, we uncovered the transcriptional network regulated by ELF3 and defined its distinctive gene signature, including AURKA, CDC25B, CLDN4, ITGB6, and YWAHB. Furthermore, a loss‐of‐function assay revealed that ELF3 depletion led to poor cell viability. Finally, using gene expression of clinical samples, we successfully divided GIS‐NEC patients into two subgroups according to the ELF3 signature and demonstrated that tumor‐promoting pathways were activated in the ELF3 signature–high group. Our findings highlight the transcriptional regulation of ELF3 as an oncogenic transcription factor and its tumor‐promoting properties in NEC.

Antibody–drug conjugates (ADCs) are emerging as a promising class of targeted cancer therapy. Trastuzumab deruxtecan (T‐DXd), a human epidermal growth factor receptor 2 (HER2)‐directed ADC, has demonstrated clinical efficacy in HER2‐positive gastric and breast cancers, as well as in HER2‐mutant non‐small cell lung cancer. However, the development of acquired resistance limits their long‐term efficacy. To elucidate the resistance mechanism, we established T‐DXd‐resistant cell lines derived from HER2‐amplified gastric xenografts (N87 acquired resistance [AR]) and leptomeningeal carcinomatosis (Calu‐3 AR) lung cancer cells. N87 AR cells exhibited cross‐resistance to T‐DXd, payload DXd, and topoisomerase I inhibitor SN‐38 despite preserved HER2 expression and intact drug internalization. As payload resistance‐related molecules, ATP‐binding cassette (ABC) transporter ABCG2 and ABCB1 were markedly upregulated in N87 AR and Calu‐3 cells, respectively. Inhibition of ABCG2 and ABCB1 in N87 AR and Calu‐3 cells, respectively, through siRNA‐mediated knockdown restored T‐DXd sensitivity in both models. As a strategy to overcome resistance, pharmacological inhibitors of ABCG2 and ABCB1 restored the T‐DXd sensitivity of N87 AR and Calu‐3 cells, respectively. Moreover, BB‐1701, a novel HER2‐ADC containing eribulin as a payload, to which N87 AR cells are sensitive, exhibited antitumor effects in N87 AR cells in vitro and in vivo. These findings indicate that ABC transporter‐mediated drug efflux is an important mechanism underlying T‐DXd resistance in HER2‐positive gastric and lung cancer models. Furthermore, our study suggests that both targeting drug efflux pathways and utilizing alternative payloads may be effective strategies for overcoming T‐DXd resistance in HER2‐positive gastric and lung cancers.

Small cell lung cancer (SCLC), an aggressive neuroendocrine carcinoma, has an extremely poor prognosis. ASCL1 and NEUROD1 are key regulators of neuroendocrine features, and previous studies have suggested that SCLC plasticity occurs during the transition from ASCL1-positive (SCLC-A) to NEUROD1-positive (SCLC-N) subtypes. In this study, we attempted to understand the transcriptional programs governed by ASCL1 and NEUROD1 to identify markers of SCLC plasticity. Immunohistochemistry and epigenome and transcriptome analyses in ASCL1/NEUROD1 double-positive SCLC cells (SCLC-A/N) revealed co-expression of ASCL1 and NEUROD1 in almost half of SCLC cases. Genome-wide profiling of histone modifications, ASCL1 and NEUROD1 binding sites, and gene co-expression patterns revealed that both ASCL1 and NEUROD1 are active in SCLC-A/N and regulate partially distinct target genes. Furthermore, SCLC-A/N exhibited characteristics that were intermediate between SCLC-A and SCLC-N subtypes. NEUROD1 knockout, followed by RNA-seq, suggested an association between NEUROD and NHLH transcription factors that might shape the NEUROD1-mediated regulatory network. Small RNA-seq further indicated that miR-139-5p is specifically expressed in NEUROD1-positive SCLC, and transcriptomic studies suggested that miR-139-5p might regulate an array of pathologically relevant genes in collaboration with other NEUROD1-associated miRNAs. Our integrative analyses provide deeper insights into SCLC heterogeneity and multi-layered transcriptional programs differentially governed by ASCL1 and NEUROD1.

Esophageal squamous cell carcinoma (ESCC) is associated with poor prognosis due to aggressive invasion and therapy resistance. Cancer-associated fibroblasts (CAFs) are key stromal components that promote tumor progression; however, their specific roles in ESCC remain unclear. Using a direct co-culture model of ESCC cell lines (TE-9, -10, and -15) and mesenchymal stem cells (MSCs) to generate CAF-like cells, we identified biglycan (BGN) as a significantly upregulated gene in CAF-like cells via cDNA microarray analysis. Public single-cell RNA sequencing data also demonstrated elevated BGN expression in CAF clusters. We confirmed that CAF-like cells exhibited elevated BGN expression and secretion at both the mRNA and protein levels. Recombinant human BGN enhanced ESCC cell proliferation and migration by activating Erk and NF-κB signaling pathways, effects abrogated by TLR4 blockade. Furthermore, BGN promoted CAF marker expression in MSCs, M2-like macrophage polarization, and enhanced proliferation and migration abilities in both cell types. Immunohistochemical analysis of 66 ESCC tissues revealed that high stromal BGN expression correlated with greater tumor invasion, lymphatic invasion, and shorter disease-free survival. These findings indicate that CAF-derived BGN promotes ESCC progression via TLR4-mediated signaling and modulates stromal cell behavior, highlighting its potential as a prognostic biomarker and therapeutic target.